[Bioclusters] RE: mpiblast 1.3 on Mac Xserve G5

[Aaron Darling]

Ian, the compiler errors you report signify that mpiBLAST is being 
compiled against an unpatched toolbox. Although it appears you patched 
and built the toolbox you should verify that the path you are giving to 
./configure --with-ncbi is the same as the path to the patched and 
compiled toolbox. (It would seem that /usr/local/ncbi is unpatched)

Also, all of the command line arguments to ./configure should be given 
in a single ./configure command, rather than the three successive 
commands you list below...

Hope that helps,
-Aaron


Ian Yi-Feng Chang wrote:

> Dear All:
> Did anyone had successfuly install mpiblast 1.3 on mac os x (Xserve G5)?
> I've some problem to install it
> I've compiled NCBI toolkit without error messages
> $patch -p1 < ../mpiblast-1.3.0/ncbi_Oct2004_evalue.patch (within the 
> 'ncbi' directory)
> $ncbi/make/makedis.csh
> $./configure with the --disable-dependency-tracking
> $./configure --disable-dependency-tracking
> $./configure --with-ncbi=/usr/local/ncbi
> $./configure --prefix=/usr/local/mpiblast
> but when I build mpiblast, it response following messages
> I also had check previous discussion about mpiblast 1.2.1, the they 
> seems sort of diffent
> could anyone help me ?
> ian chang
> mpiBlast 1.3
> NCBI Toolkit 200410 installed
> gcc (GCC) 3.3 20030304
> $make
> make all-am
> if mpicc -DHAVE_CONFIG_H -I. -I. -I. -I../include/ 
> -I/usr/local/ncbi/include/ -DUSING_MPI 
> -DINSTALL_PREFIX="\"/usr/local/mpiblast\"" -g -O2 -MT 
> mpiblast-blast_hooks.o -MD -MP -MF ".deps/mpiblast-blast_hooks.Tpo" -c 
> -o mpiblast-blast_hooks.o `test -f 'blast_hooks.c' || echo 
> './'`blast_hooks.c; \
> then mv -f ".deps/mpiblast-blast_hooks.Tpo" 
> ".deps/mpiblast-blast_hooks.Po"; else rm -f 
> ".deps/mpiblast-blast_hooks.Tpo"; exit 1; fi
> blast_hooks.c: In function `initBLAST':
> blast_hooks.c:695: error: structure has no member named 
> `query_adjustments'
> blast_hooks.c:696: error: structure has no member named 
> `effective_db_lengths'
> blast_hooks.c: In function `getQuery':
> blast_hooks.c:747: error: structure has no member named `current_queryI'
> blast_hooks.c: In function `runBLAST':
> blast_hooks.c:1455: error: structure has no member named 
> `calculate_statistics_and_exit'
> blast_hooks.c:1457: error: structure has no member named 
> `calculate_statistics_and_exit'
> blast_hooks.c:1478: error: structure has no member named `current_queryI'
> blast_hooks.c: In function `outputResults':
> blast_hooks.c:1573: error: structure has no member named 
> `calculate_statistics_and_exit'
> mpicc: No such file or directory
> make[1]: *** [mpiblast-blast_hooks.o] Error 1
> make: *** [all] Error 2
>
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